Methodology Meetings

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09 January, 2009

Expand our toolbox

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They gave us tools, powerful tools...

... but if the only tool you have is a hammer…

…then everything looks like a nail.

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The current toolbox (for the most of us):

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What we can add:

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What we can add:

BrainVoyager

AFNI

MedINRIA

Caret

Brain Voyager

www.brainvoyager.com

SPM-like (analysis of fMRI data, visualization) + deterministic DTI Windows, Linux, Macintosh Pros: unsurpassed interactivity, interfaces with Matlab, users can add plugins (ICA, Granger Causality, ....) Cons: proprietary, closed, costs money (~ 5k euro), bad documentation (but wiki), no probabilistic DTI

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AFNI

http://afni.nimh.nih.gov/

SPM-like (analysis of fMRI data, visualization) Unix/Linux Pros: free, open source, extreme flexibility Cons: basically, command line only

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MedINRIA

http://www-sop.inria.fr/ asclepios/software/MedINRIA/

MRIcro/N-like (visualization, combination) + registration + DTI tracking, combination, visualizazion etc. Windows, Linux, Macintosh Pros: free, open source, excellent for deterministic DTI Cons: no probabilistic DTI

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Caret

http://afni.nimh.nih.gov/

MRIcro/N-like (visualization, combination); 'viewing, manipulating, and analyzing surface reconstructions of the cerebral and cerebellar cortex' Windows, Linux, Macintosh Pros: free, open source, excellent for combining anatomical/funcional data. Includes PALS. Outstanding doc. Cons: huge amount of options, menus, etc.Van Essen, DC. A Population-Average, Landmark- and Surface-based (PALS) atlas of human cerebral cortex. Neuroimage, September 2005.

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R - AnalyzeFMRI

http://www.r-project.org

R ~ Matlab -> unlimited flexibility in number manipulation AnalyzeFMRI -> extract/write data from/to Analyze/NIFTI Windows, Linux, Macintosh

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R - AnalyzeFMRIsurgeon <- function(what2write, pathandname)

{

#print("sono dentro surgeon")

sizeofHdrlastpart <- 89

sizeofHdrfirstpart <- 254

Xorig <- -20

Yorig <- -8

Zorig <- -7

#data saved, but the origin defaults to 8224, 8224, 8224

f.write.analyze(what2write, pathandname, "float", c(3,3,3))

#print("scritta mappa")

#open the same file for surgery

zz<-file(paste(pathandname,".hdr",sep=""),open="rb")

#the file beginning is read and saved for the future

foobeginning <- readBin(zz, what="raw", n=sizeofHdrfirstpart, size=1)

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R - AnalyzeFMRIsurgeon <- function(what2write, pathandname)

{

#print("sono dentro surgeon")

sizeofHdrlastpart <- 89

sizeofHdrfirstpart <- 254

Xorig <- -20

Yorig <- -8

Zorig <- -7

#data saved, but the origin defaults to 8224, 8224, 8224

f.write.analyze(what2write, pathandname, "float", c(3,3,3))

#print("scritta mappa")

#open the same file for surgery

zz<-file(paste(pathandname,".hdr",sep=""),open="rb")

#the file beginning is read and saved for the future

foobeginning <- readBin(zz, what="raw", n=sizeofHdrfirstpart, size=1)

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R - AnalyzeFMRI #write origin coordinates

writeBin(as.integer(Xorig),zz,size=2)

writeBin(as.integer(Yorig),zz,size=2)

writeBin(as.integer(Zorig),zz,size=2)

#write file end

writeBin(fooend,zz)

#that's it.

close(zz)

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R - AnalyzeFMRI Random Fields N2G models Smoothing Statistical Thresholding (Bonferroni, FDR, RF) FastICA read/write Analyze/NIFTI

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Capabilities:

R - fmri read/write Analyze, NIFTI, AFNI, DICOM first level (single subject) analysis ROI definition and extraction

Tabelow, K., Polzehl, J., Voss, H.U., and Spokoiny, V. Analysing fMRI experiments with structure adaptive smoothing procedures, NeuroImage, 33:55-62 (2006).

FSLd

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S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, and P.M. Matthews. Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage, 23(S1):208-219, 2004

SPM + MRIcro/N-like Linux, plus MacOSX+X11, plus Windows+VMware Pros: free, open source, fully integrated set of tools, excellent for DTI (also probabilistic), .nii.gz Cons: requires some knowledge of programming to be used effectively

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Prof. Irene Tracey Director of FMRIB CentreProf. Steve Smith Centre DirectorProf. Peter Jezzard Department of Clinical NeurologyDr Heidi Johansen-Berg Department of Clinical NeurologyDr Matthew Rushworth Department of Experimental PsychologyProf. Andrew Parker Department of Physiology, Anatomy and GeneticsProf. Alan Cowey Department of Experimental Psychology

Jesper Andersson, Peter Bannister, Christian Beckmann, Timothy Behrens, Michael Chappell, Gwenaëlle Douaud, Ivana Drobnjak, David Flitney, Adrian Groves, Saad Jbabdi, Mark Jenkinson, Heidi Johansen-Berg, Duncan Mortimer, Rami Niazy, Tom Nichols, Brian Patenaude, Reza Salimi, Steve Smith, John Vickers, Matthew Webster, Mark Woolrich, Yongyue Zhang.

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FSL TOOLS

Functional MRI

FEAT Model-based FMRI analysis: data preprocessing (including MCFLIRT motion correction); first-level FILM GLM timeseries analysis; higher-level FLAME Bayesian mixed effects analysis.

MELODIC Model-free FMRI analysis using Probabilistic Independent Component Analysis (PICA). MELODIC automatically estimates the number of interesting noise and signal sources in the data and because of the associated "noise model", is able to assign significance ("p-values") to the output spatial maps. MELODIC can also analyse multiple subjects or sessions simultaneously using Tensor-ICA.

FLOBS Generation of optimal HRF basis functions and Bayesian activation estimation.

FABBER Fast ASL & BOLD Bayesian Estimation Routine. Efficient nonlinear modelling and estimation of BOLD and CBF from dual-echo ASL data, using Variational Bayes.

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FSL TOOLS

Structural MRI

BET Brain Extraction Tool - segments brain from non-brain in structural and functional data, and models skull and scalp surfaces.

FAST FMRIB's Automated Segmentation Tool - brain segmentation (into different tissue types) and bias field correction.

FLIRT FMRIB's Linear Image Registration Tool - linear inter- and intra-modal registration.

FNIRT FMRIB's Nonlinear Image Registration Tool - nonlinear registration.

FIRST FMRIB's Integrated Registration and Segmentation Tool. FIRST uses mesh models trained with a large amount of rich hand-segmented training data to segment subcortical brain structures.

FUGUE Unwarps geometric distortion in EPI images using B0 field maps.

SIENA Structural brain change analysis, for estimating brain atrophy.

FSL-VBM VBM-style analysis using FSL tools, for voxelwise analysis of grey-matter density.

SUSAN Nonlinear noise reduction.

FSLd

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FSL TOOLS

Diffusion MRI

FDT FMRIB's Diffusion Toolbox - tools for low-level diffusion parameter reconstruction and probabilistic tractography, including crossing-fibre modelling.

TBSS Tract-Based Spatial Statistics (part of FMRIB's Diffusion Toolbox) - voxelwise analysis of multi-subject diffusion data.

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FSL TOOLS

Miscellanea

POSSUM Physics-Oriented Simulated Scanner for Understanding MRI. An FMRI data simulator that produces realistic simulated images and FMRI time series given a gradient echo pulse sequence, a segmented object with known tissue parameters, and a motion sequence..

Inference Various inference/thresholding tools, including: SMM spatial mixture modelling - alternative hypothesis testing using histogram mixture modelling with spatial regularisation of the voxel classification into activation and non-activation; Randomise (permutation-based inference tool for nonparametric statistical thresholding); cluster (cluster-based thresholding using GRF theory for inference); FDR (false discovery rate inference) and Glm (a GUI for creating model design matrices).

FSLView Interactive display tool for 3D and 4D data.

Atlases Several complementary brain atlases, integrated into FSLView and Featquery, allowing viewing of structural and cytoarchitectonic standard space labels and probability maps for cortical and subcortical structures and white matter tracts.

FSLUTILS Misc utils for converting and processing images.

MISCVIS Simple (non-interactive) image display utilities and a stats overlay utility.

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FSL TOOLS

Atlases

* Harvard-Oxford cortical and subcortical structural atlases * Jülich histological atlas * JHU DTI-based white-matter atlases * Oxford thalamic connectivity atlas * Talairach atlas * MNI structural atlas

FSLd

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FSL TOOLS

FSLUTILS

fslchfiletype - used to change the file type of an image (e.g. from ANALYZE_GZ to NIFTI). The first argument is the desired file type (one of ANALYZE, ANALYZE_GZ, NIFTI, NIFTI_GZ, NIFTI_PAIR, NIFTI_PAIR_GZ)

fslcpgeom - copy certain parts of the header information (image dimensions, voxel dimensions, voxel dimensions units string, image orientation/origin or qform/sform info) from one image to another.

fslmaths - simple but powerful program to allow mathematical manipulation of images.

fslmerge - concatenate image files into a single output. This concatenation can be in time, or in X, Y or Z.

fslroi - extract region of interest (ROI) from an image. You can a) take a 3D ROI from a 3D data set (or if it is 4D, the same ROI is taken from each time point and a new 4D data set is created), b) extract just some time points from a 4D data set, or c) control time and space limits to the ROI.

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FSLMATHS

Binary operations:

-add -sub -mul -div : add/subtract/multiply/divide current image by following input

-rem : modulus remainder - divide current image by following input and take remainder

-mas : use (following image>0) to mask current image

-thr : use following number to threshold current image (zero anything below the number)

-thrp : use following percentage (0-100) of ROBUST RANGE to threshold current image (zero anything below the number)

-thrP : use following percentage (0-100) of ROBUST RANGE of non-zero voxels and threshold below

-uthr : use following number to upper-threshold current image (zero anything above the number)

-uthrp : use following percentage (0-100) of ROBUST RANGE to upper-threshold current image (zero anything above the number)

-uthrP : use following percentage (0-100) of ROBUST RANGE of non-zero voxels and threshold above

-max : take maximum of following input and current image

-min : take minimum of following input and current image

FSL - fslmathsd

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Unary operations:

-exp : exponential -log : natural logarithm -sqr : square -sqrt : square root -abs : absolute value -bin : use (current image>0) to binarise -index : replace each nonzero voxel with a unique (subject to wrapping) index number -grid <value> <spacing> : add a 3D grid of intensity <value> with grid spacing <spacing> -edge : edge strength -tfce <H> <E> <connectivity>: enhance with TFCE, e.g. -tfce 2 0.5 6 (maybe change 6 to 26 for skeletons) -nan : replace NaNs (improper numbers) with 0 -nanm : make NaN (improper number) mask with 1 for NaN voxels, 0 otherwise -inm <mean> : (-i i ip.c) intensity normalisation (per 3D volume mean) -ing <mean> : (-I i ip.c) intensity normalisation, global 4D mean)

FSL - fslmathsd

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Kernel operations:

-kernel 3D : 3x3x3 box centered on target voxel (set as default kernel) -kernel 2D : 3x3x1 box centered on target voxel -kernel box <size> : all voxels in a box of width <size> centered on target voxel -kernel boxv <size> : <size>x<size>x<size> box centered on target voxel, CAUTION: size should be an odd number -kernel gauss <sigma> : gaussian kernel (sigma in mm, not voxels) -kernel sphere <size> : all voxels in a sphere of radius <size> mm centered on target voxel -kernel file <filename> : use external file as kernel

FSL - fslmathsd

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Spatial Filtering operations:

-dilM : Mean Dilation of zero voxels (using non-zero voxels in kernel) -dilD : Modal Dilation of zero voxels (using non-zero voxels in kernel) -dilF : Maximum filtering of all voxels -ero : Erode by zeroing non-zero voxels when zero voxels found in kernel -eroF : Minimum filtering of all voxels -fmedian : Median Filtering -fmean : Mean filtering, kernel weighted (conventionally used with gauss kernel) -fmeanu : Mean filtering, kernel weighted, un-normalised (gives edge effects) -s <sigma> : create a gauss kernel of sigma mm and perform mean filtering -subsamp2 : downsamples image by a factor of 2 (keeping new voxels centred on old) -subsamp2offc : downsamples image by a factor of 2 (non-centred)

FSL - /usr/loca/fsl/bind

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FSL - scriptingd

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Strategy: Create a mask, add 2, mask the result

Task: add 2 to all non-zero voxels of all images in a given folder

Implementation in a bash script using fslmaths

FSL - scriptingd

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Task: bring anatomies in standard space

Implementation in a bash script using flirt